Is personalized medicine here?

ONCOLOGY (United States)

Volumn 30, Issue 4, 2016, Pages

  Carneiro, Benedito A ^a,b   Costa, Ricardo ^a,b   Taxter, Timothy ^a,b   Chandra, Sunandana ^a,b   Chae, Young Kwang ^a,b   Cristofanilli, Massimo ^a,b   Giles, Francis J ^a,b  

^a Northwestern University Feinberg School of Medicine   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALECTINIB; CARBOPLATIN; CERITINIB; CRIZOTINIB; DABRAFENIB; DACARBAZINE; ERLOTINIB; LAPATINIB; MAMMALIAN TARGET OF RAPAMYCIN INHIBITOR; NIVOLUMAB; PEMBROLIZUMAB; PROTEIN TYROSINE KINASE INHIBITOR; SELUMETINIB; SUNITINIB; TUMOR MARKER; VELIPARIB; VEMURAFENIB;

BREAST CANCER; CANCER DIAGNOSIS; CANCER GENETICS; CANCER IMMUNOTHERAPY; CANCER INCIDENCE; CANCER PROGNOSIS; CANCER RECURRENCE; CANCER THERAPY; CIRCULATING TUMOR CELL; DISTANT METASTASIS FREE SURVIVAL; DRUG EFFICACY; EPIGENETICS; HUMAN; MASS SPECTROMETRY; METABOLOMICS; NEXT GENERATION SEQUENCING; NON SMALL CELL LUNG CANCER; OVERALL SURVIVAL; PERSONALIZED MEDICINE; PHASE 2 CLINICAL TRIAL (TOPIC); PHASE 3 CLINICAL TRIAL (TOPIC); POLYMERASE CHAIN REACTION; PROGRESSION FREE SURVIVAL; RANDOMIZED CONTROLLED TRIAL (TOPIC); RECURRENCE FREE SURVIVAL; REVIEW; SOLID TUMOR; TRANSCRIPTOMICS; TREATMENT RESPONSE;

EID: 84964294682     PISSN: 08909091     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (105)

1. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513:202-9
2. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61-70
3. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013;499:43-9
4. Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511:543-50
5. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014;507:315-22
6. Jakob JA, Bassett RL Jr., Ng CS, et al. NRAS mutation status is an independent prognostic factor in metastatic melanoma. Cancer. 2012;118:4014-23
7. Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364:2507-16
8. Hauschild A, Grob JJ, Demidov LV, et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2012;380:358-65
9. Herbst RS, Heymach JV, Lippman SM. Lung cancer. N Engl J Med. 2008;359:1367-80
10. Zhou C, Wu YL, Chen G, et al. Final overall survival results from a randomised, phase III study of erlotinib versus chemotherapy as first-line treatment of EGFR mutation-positive advanced non-small-cell lung cancer (OPTIMAL, CTONG-0802). Ann Oncol. 2015;26:1877-83
11. Fukuoka M, Wu YL, Thongprasert S, et al. Biomarker analyses and final overall survival results from a phase III, randomized, open-label, first-line study of gefitinib versus carboplatin/paclitaxel in clinically selected patients with advanced non-small-cell lung cancer in Asia (IPASS). J Clin Oncol. 2011;29:2866-74
12. Sequist LV, Yang JC, Yamamoto N, et al. Phase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutations. J Clin Oncol. 2013;31:3327-34
13. Soda M, Choi YL, Enomoto M, et al. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature. 2007;448:561-6
14. Solomon BJ, Mok T, Kim DW, et al. First-line crizotinib versus chemotherapy in ALK-positive lung cancer. N Engl J Med. 2014;371:2167-77
15. Schwaederle M, Parker BA, Schwab RB, et al. Molecular tumor board: the University of California-San Diego Moores Cancer Center experience. Oncologist. 2014;19:631-6
16. Tafe LJ, Gorlov IP, de Abreu FB, et al. Implementation of a molecular tumor board: the impact on treatment decisions for 35 patients evaluated at Dartmouth-Hitchcock Medical Center. Oncologist. 2015;20:1011-8
17. Carneiro BA, Elvin JA, Kamath SD, et al. FGFR3-TACC3: a novel gene fusion in cervical cancer. Gynecol Oncol Rep. 2015;13:53-6
18. Chen S, Li S, Xie W, et al. Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy. PLoS One. 2014;9:e92192
19. Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30:434-9
20. Frampton GM, Fichtenholtz A, Otto GA, et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol. 2013;31:1023-31
21. Vogelstein B, Kinzler KW. The path to cancer—three strikes and you’re out. N Engl J Med. 2015;373:1895-8
22. Van Allen EM, Wagle N, Stojanov P, et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014;20:682-8
23. Postel-Vinay S, Boursin Y, Massard C, et al. Seeking the driver in tumours with apparent normal molecular profile on comparative genomic hybridization and targeted gene panel sequencing: What is the added value of whole exome sequencing? Ann Oncol. 2016;27:344-52
24. Thon N, Kreth S, Kreth FW. Personalized treatment strategies in glioblastoma: MGMT promoter methylation status. Onco Targets Ther. 2013;6:1363-72
25. Masser DR, Stanford DR, Freeman WM. Targeted DNA methylation analysis by next-generation sequencing. J Vis Exp. 2015;96:52488
26. Chan KC, Jiang P, Chan CW, et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci USA. 2013;110:18761-8
27. Biselli-Chicote PM, Oliveira AR, Pavarino EC, Goloni-Bertollo EM. VEGF gene alternative splicing: pro-and anti-angiogenic isoforms in cancer. J Cancer Res Clin Oncol. 2012;138:363-70
28. Pal S, Gupta R, Davuluri RV. Alternative transcription and alternative splicing in cancer. Pharmacol Ther. 2012;136:283-94
29. Kim KT, Lee HW, Lee HO, et al. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol. 2015;16:127
30. Brosseau JP, Lucier JF, Nwilati H, et al. Tumor microenvironment-associated modifications of alternative splicing. RNA. 2014;20:189-201
31. Oesper L, Satas G, Raphael BJ. Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinformatics. 2014;30:3532-40
32. Li Y, Xie X. A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. BMC Bioinformatics. 2013;14(suppl 5):S11
33. Cieslik M, Chugh R, Wu YM, et al. The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing. Genome Res. 2015;25:1372-81
34. Bardelli A, Corso S, Bertotti A, et al. Amplification of the MET receptor drives resistance to anti-EGFR therapies in colorectal cancer. Cancer Discov. 2013;3:658-73
35. Wilmott JS, Long GV, Howle JR, et al. Selective BRAF inhibitors induce marked T-cell infiltration into human metastatic melanoma. Clin Cancer Res. 2012;18:1386-94
36. Spranger S, Bao R, Gajewski TF. Melanoma-intrinsic beta-catenin signalling prevents anti-tumour immunity. Nature. 2015;523:231-5
37. Atkins MB, Larkin J. Immunotherapy combined or sequenced with targeted therapy in the treatment of solid tumors: current perspectives. J Natl Cancer Inst. 2016 Feb 2. [Epub ahead of print]
38. Gerlinger M, Rowan AJ, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366:883-92
39. Ignatiadis M, Lee M, Jeffrey SS. Circulating tumor cells and circulating tumor DNA: challenges and opportunities on the path to clinical utility. Clin Cancer Res. 2015;21:4786-800
40. Cristofanilli M, Budd GT, Ellis MJ, et al. Circulating tumor cells, disease progression, and survival in metastatic breast cancer. N Engl J Med. 2004;351:781-91
41. Smerage JB, Barlow WE, Hortobagyi GN, et al. Circulating tumor cells and response to chemotherapy in metastatic breast cancer: SWOG S0500. J Clin Oncol. 2014;32:3483-9
42. Scher HI, Heller G, Molina A, et al. Circulating tumor cell biomarker panel as an individual-level surrogate for survival in metastatic castration-resistant prostate cancer. J Clin Oncol. 2015;33:1348-55
43. de Bono JS, Scher HI, Montgomery RB, et al. Circulating tumor cells predict survival benefit from treatment in metastatic castration-resistant prostate cancer. Clin Cancer Res. 2008;14:6302-9
44. Cohen SJ, Punt CJ, Iannotti N, et al. Relationship of circulating tumor cells to tumor response, progression-free survival, and overall survival in patients with metastatic colorectal cancer. J Clin Oncol. 2008;26:3213-21
45. Pestrin M, Bessi S, Puglisi F, et al. Final results of a multicenter phase II clinical trial evaluating the activity of single-agent lapatinib in patients with HER2-negative metastatic breast cancer and HER2-positive circulating tumor cells. A proof-of-concept study. Breast Cancer Res Treat. 2012;134:283-9
46. Diehl F, Diaz LA Jr. Digital quantification of mutant DNA in cancer patients. Curr Opin Oncol. 2007;19:36-42
47. Nygaard AD, Holdgaard PC, Spindler KL, et al. The correlation between cell-free DNA and tumour burden was estimated by PET/CT in patients with advanced NSCLC. Br J Cancer. 2014;110:363-8
48. Forshew T, Murtaza M, Parkinson C, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012;4:136ra68
49. Dawson SJ, Tsui DW, Murtaza M, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013;368:1199-209
50. Garcia-Murillas I, Schiavon G, Weigelt B, et al. Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. Sci Transl Med. 2015;7:302ra133
51. Tie J, Kinde I, Wang Y, et al. Circulating tumor DNA (ctDNA) as a marker of recurrence risk in stage II colon cancer (CC). J Clin Oncol. 2014;32(suppl 5s):abstr 11015
52. Murtaza M, Dawson SJ, Tsui DW, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013;497:108-12
53. Cravatt BF, Simon GM, Yates JR 3rd. The biological impact of mass-spectrometry-based proteomics. Nature. 2007;450:991-1000
54. Kim Y, Ignatchenko V, Yao CQ, et al. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics. 2012;11:1870-84
55. Principe S, Jones EE, Kim Y, et al. In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. Proteomics. 2013;13:1667-71
56. Stock J. The emerging role of lipidomics. Atherosclerosis. 2012;221:38-40
57. Kim IC, Lee JH, Bang G, et al. Lipid profiles for HER2-positive breast cancer. Anticancer Res. 2013;33:2467-72
58. Zhang A, Sun H, Yan G, et al. Metabolomics in diagnosis and biomarker discovery of colorectal cancer. Cancer Lett. 2014;345:17-20
59. Buas MF, Gu H, Djukovic D, et al. Identification of novel candidate plasma metabolite biomarkers for distinguishing serous ovarian carcinoma and benign serous ovarian tumors. Gynecol Oncol. 2016;140:138-44
60. Giskeodegard GF, Hansen AF, Bertilsson H, et al. Metabolic markers in blood can separate prostate cancer from benign prostatic hyperplasia. Br J Cancer. 2015;113:1712-9
61. Kaddurah-Daouk R, Weinshilboum R. Metabolomic signatures for drug response phenotypes: pharmacometabolomics enables precision medicine. Clin Pharmacol Ther. 2015;98:71-5
62. Backshall A, Sharma R, Clarke SJ, Keun HC. Pharmacometabonomic profiling as a predictor of toxicity in patients with inoperable colorectal cancer treated with capecitabine. Clin Cancer Res. 2011;17:3019-28
63. Burstein HJ, Mangu PB, Somerfield MR, et al. American Society of Clinical Oncology clinical practice guideline update on the use of chemotherapy sensitivity and resistance assays. J Clin Oncol. 2011;29:3328-30
64. Cree IA, Kurbacher CM, Lamont A, et al; TCA Ovarian Cancer Trial Group. A prospective randomized controlled trial of tumour chemosensitivity assay directed chemotherapy versus physician's choice in patients with recurrent platinum-resistant ovarian cancer. Anticancer Drugs. 2007;18:1093-101
65. Friedman AA, Letai A, Fisher DE, Flaherty KT. Precision medicine for cancer with next-generation functional diagnostics. Nat Rev Cancer. 2015;15:747-56
66. Stebbing J, Paz K, Schwartz GK, et al. Patient-derived xenografts for individualized care in advanced sarcoma. Cancer. 2014;120:2006-15
67. Hidalgo M, Bruckheimer E, Rajeshkumar NV, et al. A pilot clinical study of treatment guided by personalized tumorgrafts in patients with advanced cancer. Mol Cancer Ther. 2011;10:1311-6
68. Schwaederle M, Zhao M, Lee JJ, et al. Impact of precision medicine in diverse cancers: a meta-analysis of phase II clinical trials. J Clin Oncol. 2015;33:3817-25
69. Jardim DL, Schwaederle M, Wei C, et al. Impact of a biomarker-based strategy on oncology drug development: a meta-analysis of clinical trials leading to FDA approval. J Natl Cancer Inst. 2015 Sep 15. [Epub ahead of print]
70. Le Tourneau C, Delord JP, Goncalves A, et al. Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial. Lancet Oncol. 2015;16:1324-34
71. Redig AJ, Janne PA. Basket trials and the evolution of clinical trial design in an era of genomic medicine. J Clin Oncol. 2015;33:975-7
72. Hyman DM, Puzanov I, Subbiah V, et al. Vemurafenib in multiple nonmelanoma cancers with BRAF V600 mutations. N Engl J Med. 2015;373:726-36
73. Lopez-Chavez A, Thomas A, Rajan A, et al. Molecular profiling and targeted therapy for advanced thoracic malignancies: a biomarker-derived, multiarm, multihistology phase II basket trial. J Clin Oncol. 2015;33:1000-7
74. Rodon J, Saura C, Dienstmann R, et al. Molecular prescreening to select patient population in early clinical trials. Nat Rev Clin Oncol. 2012;9:359-66
75. Herbst RS, Gandara DR, Hirsch FR, et al. Lung Master Protocol (Lung-MAP)—a biomarker-driven protocol for accelerating development of therapies for squamous cell lung cancer: SWOG S1400. Clin Cancer Res. 2015;21:1514-24
76. Steuer CE, Papadimitrakopoulou V, Herbst RS, et al. Innovative clinical trials: the LUNG-MAP study. Clin Pharmacol Ther. 2015;97:488-91
77. Berry DA. Bayesian clinical trials. Nat Rev Drug Discov. 2006;5:27-36
78. Rugo HS, Olopade O, DeMichele A, et al. Veliparib/carboplatin plus standard neoadjuvant therapy for high-risk breast cancer: first efficacy results from the I-SPY 2 trial. Cancer Res. 2013;73(suppl 24):abstr S5-02
79. Glimelius B, Lahn M. Window-of-opportunity trials to evaluate clinical activity of new molecular entities in oncology. Ann Oncol. 2011;22:1717-25
80. Hunter DJ, Khoury MJ, Drazen JM. Letting the genome out of the bottle—will we get our wish? N Engl J Med. 2008;358:105-7
81. Simon RM, Paik S, Hayes DF. Use of archived specimens in evaluation of prognostic and predictive biomarkers. J Natl Cancer Inst. 2009;101:1446-52
82. Brahmer J, Reckamp KL, Baas P, et al. Nivolumab versus docetaxel in advanced squamous-cell non-small-cell lung cancer. N Engl J Med. 2015;373:123-35
83. Borghaei H, Paz-Ares L, Horn L, et al. Nivolumab versus docetaxel in advanced nonsquamous non-small-cell lung cancer. N Engl J Med. 2015;373:1627-39
84. Wang C, Thudium KB, Han M, et al. In vitro characterization of the anti-PD-1 antibody nivolumab, BMS-936558, and in vivo toxicology in non-human primates. Cancer Immunol Res. 2014;2:846-56
85. Robert C, Long GV, Brady B, et al. Nivolumab in previously untreated melanoma without BRAF mutation. N Engl J Med. 2015;372:320-30
86. Motzer RJ, Escudier B, McDermott DF, et al. Nivolumab versus everolimus in advanced renal cell carcinoma. N Engl J Med. 2015;373:1803-13
87. Powles T, Eder JP, Fine GD, et al. MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer. Nature. 2014;515:558-62
88. Hamanishi J, Mandai M, Ikeda T, et al. Safety and antitumor activity of anti-PD-1 antibody, nivolumab, in patients with platinum-resistant ovarian cancer. J Clin Oncol. 2015;33:4015-22
89. Le DT, Uram JN, Wang H, et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med. 2015;372:2509-20
90. Segal NH, Parsons DW, Peggs KS, et al. Epitope landscape in breast and colorectal cancer. Cancer Res. 2008;68:889-92
91. Nagalla S, Chou JW, Willingham MC, et al. Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. Genome Biol. 2013;14:R34
92. Tran E, Turcotte S, Gros A, et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science. 2014;344:641-5
93. Carreno BM, Magrini V, Becker-Hapak M, et al. Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science. 2015;348:803-8
94. Snyder A, Makarov V, Merghoub T, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med. 2014;371:2189-99
95. Rizvi NA, Hellmann MD, Snyder A, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348:124-8
96. Kensler TW, Spira A, Garber JE, et al. Transforming cancer prevention through precision medicine and immune-oncology. Cancer Prev Res (Phila). 2016;9:2-10.
97. http://www.cancernetwork.com/review-article
98. http://www.cancernetwork.com/oncology-journal
99. http://www.cancernetwork.com/authors/benedito-carneiro-md-msc
100. http://www.cancernetwork.com/authors/ricardo-costa-md-msc
101. http://www.cancernetwork.com/authors/timothy-taxter-md
102. http://www.cancernetwork.com/authors/sunandana-chandra-md
103. http://www.cancernetwork.com/authors/young-kwang-chae-md
104. http://www.cancernetwork.com/authors/massimo-cristofanilli-md-0
105. http://www.cancernetwork.com/authors/francis-j-giles-mb-md